I think he was using the time to talk to Cena about what they needed to do. Whether you like Cena or not, Shawn had the worst PPV match of his life with him. I get the feeling that Shawn was supposed to win right up until before the match, hence the reason he was angry during it. Cena didnt sell the leg injury, fair enough but Vince says who wins and who doesnt and the ref is told by Vince on the earpiece what to do.
It did look a bit suss to me though :D I will promise you that they will have a better match at Backlash. Cena would have apologised to Shawn backstage, man to man, and while he may be in the dog box for a while, Cena respects him and the last thing he wants to do is diminish Shawn's PPV quality.